Job ID = 6454036 SRX = SRX1794222 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:40:32 prefetch.2.10.7: 1) Downloading 'SRR3575256'... 2020-06-21T08:40:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:41:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:41:41 prefetch.2.10.7: 'SRR3575256' is valid 2020-06-21T08:41:41 prefetch.2.10.7: 1) 'SRR3575256' was downloaded successfully Read 10926568 spots for SRR3575256/SRR3575256.sra Written 10926568 spots for SRR3575256/SRR3575256.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:38 10926568 reads; of these: 10926568 (100.00%) were unpaired; of these: 310261 (2.84%) aligned 0 times 8748647 (80.07%) aligned exactly 1 time 1867660 (17.09%) aligned >1 times 97.16% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1333306 / 10616307 = 0.1256 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:48:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:48:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:15: 1000000 INFO @ Sun, 21 Jun 2020 17:48:20: 2000000 INFO @ Sun, 21 Jun 2020 17:48:25: 3000000 INFO @ Sun, 21 Jun 2020 17:48:30: 4000000 INFO @ Sun, 21 Jun 2020 17:48:34: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:48:39: 6000000 INFO @ Sun, 21 Jun 2020 17:48:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:48:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:44: 7000000 INFO @ Sun, 21 Jun 2020 17:48:46: 1000000 INFO @ Sun, 21 Jun 2020 17:48:50: 8000000 INFO @ Sun, 21 Jun 2020 17:48:51: 2000000 INFO @ Sun, 21 Jun 2020 17:48:55: 9000000 INFO @ Sun, 21 Jun 2020 17:48:55: 3000000 INFO @ Sun, 21 Jun 2020 17:48:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:48:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:48:57: #1 total tags in treatment: 9283001 INFO @ Sun, 21 Jun 2020 17:48:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:48:57: #1 tags after filtering in treatment: 9282831 INFO @ Sun, 21 Jun 2020 17:48:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:58: #2 number of paired peaks: 9078 INFO @ Sun, 21 Jun 2020 17:48:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:58: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:59: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 17:48:59: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 17:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.05_model.r INFO @ Sun, 21 Jun 2020 17:48:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:00: 4000000 INFO @ Sun, 21 Jun 2020 17:49:05: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 17:49:10: 6000000 INFO @ Sun, 21 Jun 2020 17:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 17:49:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:15: 7000000 INFO @ Sun, 21 Jun 2020 17:49:16: 1000000 INFO @ Sun, 21 Jun 2020 17:49:20: 2000000 INFO @ Sun, 21 Jun 2020 17:49:21: 8000000 INFO @ Sun, 21 Jun 2020 17:49:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:25: 3000000 INFO @ Sun, 21 Jun 2020 17:49:26: 9000000 INFO @ Sun, 21 Jun 2020 17:49:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:49:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:49:27: #1 total tags in treatment: 9283001 INFO @ Sun, 21 Jun 2020 17:49:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:49:28: #1 tags after filtering in treatment: 9282831 INFO @ Sun, 21 Jun 2020 17:49:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:29: #2 number of paired peaks: 9078 INFO @ Sun, 21 Jun 2020 17:49:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:29: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 17:49:29: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 17:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.10_model.r INFO @ Sun, 21 Jun 2020 17:49:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:30: 4000000 INFO @ Sun, 21 Jun 2020 17:49:35: 5000000 INFO @ Sun, 21 Jun 2020 17:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:37: Done! pass1 - making usageList (233 chroms): 3 millis pass2 - checking and writing primary data (9907 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:40: 6000000 INFO @ Sun, 21 Jun 2020 17:49:45: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:49:50: 8000000 INFO @ Sun, 21 Jun 2020 17:49:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:55: 9000000 INFO @ Sun, 21 Jun 2020 17:49:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:49:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:49:56: #1 total tags in treatment: 9283001 INFO @ Sun, 21 Jun 2020 17:49:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:49:57: #1 tags after filtering in treatment: 9282831 INFO @ Sun, 21 Jun 2020 17:49:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:58: #2 number of paired peaks: 9078 INFO @ Sun, 21 Jun 2020 17:49:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:58: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:58: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:58: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:58: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 17:49:58: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 17:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.20_model.r INFO @ Sun, 21 Jun 2020 17:49:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.10_summits.bed INFO @ Sun, 21 Jun 2020 17:50:06: Done! pass1 - making usageList (159 chroms): 2 millis pass2 - checking and writing primary data (8080 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:50:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794222/SRX1794222.20_summits.bed INFO @ Sun, 21 Jun 2020 17:50:34: Done! pass1 - making usageList (96 chroms): 2 millis pass2 - checking and writing primary data (5482 records, 4 fields): 9 millis CompletedMACS2peakCalling